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Mathematics in Conservation: p1
The Case of the Endangered 2N
μ
Florida Panther σ
by
Gefrey F. Stopper, Department of Biology Tlost
Andrew G. Lazowski, Department of Mathematics
Sacred Heart University, Fairfeld, CT

Part I – Endangered Species

As human population sizes increase around the world, we are constantly changing, depleting, and fragmenting habitats
of wild species. Tis habitat change and fragmentation is especially detrimental to large mammals that tend to require
large habitable ranges in which to survive, are long-lived, and produce few ofspring per year.
As of November 2010, in the United States alone there were 414 animal species listed as endangered (www.fws.gov),
meaning that they are “in danger of extinction throughout all or a signifcant portion of [their] range” (uscode.house.
gov/ United States Code, Title 16, Chapter 35). Tese include species of bears, deer, bats, wolves, seals, whales, and
large cats (among many others). Te group of large cats includes the interesting case of the Florida panther.
In the mid-1990s, the Florida panther had reached critically low levels, with only 20 to 30 animals remaining in the
wild (Johnson et al. 2010; Packer 2010).
It turns out that mathematics is incredibly important in informing our understanding of the biological dynamics of
these populations. Mathematical modeling can help us understand the likelihood of extinction in a threatened or
endangered population, and is critical in our planning for their continued survival. Here we will investigate some of
the important mathematical principles underlying our understanding of the genetics of animal populations, especially
as those principles apply to conservation of endangered species, using the Florida panther as an example.

Figure 1. Te Florida panther. Photo by Connie Bransilver, USFWS/Southeast, (CC

BY 2.0), http://www.fickr.com/photos/usfwssoutheast/with/5164633462/.

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Part II – Basic Genetics

All organisms have a set of genetic instructions by which Chromosome 1 Chromosome 2
they are built. Tese instructions are written in the Chromosome 1
From Father
Chromosome 1
From Mother
Chromosome 2
From Father
Chromosome 2
From Mother
language of DNA. Te full set of instructions for any Gene/Locus D
Gene/Locus A
one organism makes up that organism’s genome. Tis
Gene/Locus B
genome—the entire set of instructions—is found in Gene/Locus E

every single cell of multicellular organisms (with the

exception of a few types of cells). Gene/Locus C
Gene/Locus F
In organisms, including humans and Florida panthers,
the genome is made of many long strings of DNA called Gene/Locus G
chromosomes (Figure 2). Each of these chromosomes has
many genes. Te genes are the specifc sections of the
Figure 2. Schematic of a hypothetical animal genome. For each
chromosomes that are responsible for making proteins, chromosome there is a copy that is inherited from one’s mother and
and so it’s the genes that control the vast majority of a copy that is inherited from one’s father. Note: In real animals, there
what happens in the organism developmentally and are usually many more chromosomes, each chromosome contains
physiologically. Between these gene regions of the many more genes, and a much larger portion of each chromosome is
non-gene DNA than suggested here.
chromosome, there is a lot of DNA that is not part
of any gene (Figure 2). Each specifc gene is reliably
found at a specifc location, or locus, on a specifc
chromosome. Because the animal inherits one copy
of each chromosome from its father and one copy of
Chromosome 1
Chromosome 1 Chromosome 1
each chromosome from its mother, each animal has two
From Father From Mother
copies of each gene.
Within a population, each gene may potentially have Gene/Locus A Allele A1 Allele A2 Heterozygote
many variant types of that gene. Tis assortment of
types is the basis of the variability in many characteristics Gene/Locus B Allele B1 Allele B1 Homozygote
among humans, such as eye color, hair color, and height.
Tese diferent types or varieties of genes are called alleles. Figure 3. Zoomed view of two copies of chromosome 1 (from top left
Because each individual has two copies of each gene, of Figure 2). Diferent allele designations at locus A (A1 and A2) show
that this individual has inherited diferent versions (alleles) of the
each individual can either have two of the same allele, gene from its mother and its father at this locus. It is, therefore, called
or the individual can have two diferent alleles. An a heterozygote for gene A. At locus B, however, this individual has
individual that has two of the same allele at a locus is inherited the same version (allele) of the gene from both its mother
called a homozygote, or is said to be homozygous for that and father (B1 and B1). It is homozygous for gene B.
gene (Figure 3). An individual that has two diferent
alleles at a locus is called a heterozygote, or is said to be
heterozygous for that gene (Figure 3). Tis designation of
the types of alleles an individual has at a locus is called Parent Gametes
its genotype. (sperm or eggs)
When an individual reproduces, that individual makes A1 A2
new versions of each chromosome for its ofspring. Tis
new version of each chromosome is a hybrid of that
A1 A2 A2
A2
individual’s two copies of the chromosome that the A1 A1
individual inherited from its own parents. Each gamete
(egg or sperm) receives one of these hybrid chromosomes
Figure 4. Passing of alleles into gametes. For each gene/locus, a parent
from the parent. Te result of this is that each gamete
passes one of its two alleles into each gamete. Note that every gamete
randomly receives one of the two alleles of each gene will receive one allele from each locus, but here we are focusing only
from that parent (Figure 4). on locus A.

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Question 1
Given that the passing of alleles into gametes is random, if we observe one gamete (egg or sperm) of an individual at a
specifc gene/locus:
a. What is the probability that the allele in that gamete is the one from the father of the individual making the
gametes?
b. What is the probability that the allele in that gamete is the one from the mother of the individual making the
gametes?
Wait
When two animals—such as Florida panthers—reproduce to make an ofspring, one gamete from the mother and one
gamete from the father fuse, so that the ofspring has two alleles for each gene/locus. It turns out that if we make a few
assumptions about a population (e.g., that mate pairings in the parent generation are random, there is no mutation,
and a few others), we can make an abstraction of the population that allows us not to worry about the specifc pairings
of alleles within specifc individuals, and instead only pay attention to frequency (or proportion) of alleles in each
population (Figure 5).

A Generation of Individuals in a Population

A1A1 A1A1 A1A2 A1A2 A2A2

The Alleles Present in That Generation

A1 A1 A1 A1 A1 A2 A1 A2 A2 A2
Figure 5. Abstraction of a population represented as only alleles, rather than individuals.
Te top row shows the allele pairings (genotypes) in individuals. Te bottom row shows the
alleles present in the population without respect to individuals.

Question 2
a. In Figure 5, what is the frequency of Allele A1 in the population (i.e., what proportion of the alleles at Locus A
are of the type A1 )?
b. In Figure 5, what is the frequency of Allele A2 in the population (i.e., what proportion of the alleles at Locus A
are of the type A2)?
Wait
If we abstract the population to allele frequencies as above, we now have a lot of power to calculate the probabilities
of certain genotypes in the next generation. Given our assumptions about random mating, we can say that every allele
in individuals in the next generation is selected randomly from the alleles available in the parent generation. Consider
the selection of allele A1 a “success,” therefore the selection of A2 is considered a “failure.” Each individual ofspring
samples twice (once for the allele inherited from each of its two parents) from the alleles that are available in the
previous generation. So if A1 and A2 are present with equal frequencies in the parent generation, then the probability
of “success” is equal to the probability of “failure,” which is 0.5. Te probability of having a homozygote for allele A1
would be the probability of getting two “successes.” Te probability of having a homozygote for allele A2 would be the
probability of getting two “failures.” Te probability of having a heterozygote would involve getting one “success” and
one “failure.” Note that there are two ways of getting the heterozygote (A1 A2 or A2A1 ).

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Question 3
Given that the population depicted in Figure 5 reproduces to make a generation of ofspring and using the allele
frequencies you calculated for that population:
a. What distribution can be used to calculate these probabilities?
b. What is the probability of an individual in the ofspring generation being homozygous for A1?
c. What is the probability of an individual in the ofspring generation being homozygous for A2?
d. What is the probability of an individual in the ofspring generation being heterozygous?

Wait
Back to the Florida Panther
Now let’s return to our population of Florida panthers. Our goal here, as with most species conservation eforts, is to
keep the population from going extinct. From many biological studies, we know that the extinction of a population
becomes more likely as a population becomes smaller. Tis is true for several reasons. One is the obvious fact that, in
a population with few individuals, an environmental challenge to the population (e.g., a natural disaster, disease, etc.)
is more likely to kill all of the individuals. But this is not the only reason that having a small population is bad for
avoiding extinction.
Tere are two other signifcant reasons that small populations are bad for avoiding extinction.
1. Small populations are more likely to lose alleles due to genetic drift.
2. Small populations are forced into inbreeding.

Genetic Variation and Genetic Drift

Small populations are more likely to lose alleles due to genetic drift. Genetic drift is change in allele frequencies due
to chance. Species/populations that reproduce by having sex appear to beneft from having a great variety of alleles
in the population (in fact, there’s a good chance that sex evolved in order to increase genetic variation in the species/
population). Genetic drift exhibits its efect primarily on alleles that are neutral (that is, they are not benefcial or
detrimental to the population). Te fact that allele frequencies can change due to randomness from one generation to
another should be clear from the exercises you did above, where allele frequencies in one generation infuence, but do
not absolutely determine, allele frequencies in the following generation.
To illustrate genetic drift, let’s focus on a specifc gene/locus with neutral alleles. For any given allele at that locus, we
can determine the probability that it will eventually disappear from the population. Because these alleles are inherited
directly from an individual’s parents, once an allele disappears from the population, it is gone forever (except in the
incredibly unlikely event that it is re-created by another mutation, the probability of which is negligible and can be
statistically ignored). We can also determine the probability that a given allele will eventually become the only allele
for that gene/locus in the population. If it becomes the only allele, we say that it is fxed, or that it has reached fxation.
It is important to realize that an allele reaching fxation in a population means that all other alleles at that gene/locus
have been lost forever from the population!
For any given point in time, the probability that an allele eventually becomes fxed in the population is exactly equal to
its proportion in the population. And the probability that it will disappear from the population is exactly one minus
its proportion in the population.

Question 4
Given the population we used in the example above, answer the following:
a. What is the probability that Allele A1 eventually becomes fxed in the population?
b. What is the probability that Allele A1 eventually disappears from the population?

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c. What is the probability that Allele A2 eventually becomes fxed in the population?
d. What is the probability that Allele A2 eventually disappears from the population?

Wait
Note that these above probabilities are true regardless of population size. But it turns out that population size has
a drastic efect on how quickly an allele disappears or goes to fxation—the smaller the population size, the more
drastically genetic drift afects the population by eliminating allelic variation from the population. As we discussed
briefy above, and will discuss in more detail below, variation is generally good for a population, and so the loss of
variation is bad for the population. Tis is important for our panther population, because the small population of
panthers means that alleles across the entire genome will disappear quickly.
How drastically does the size of a population afect how quickly alleles are lost or fxed? Tere are two types of
calculations that we can do to understand the efect of small population size.
First, we’ll consider how the population size afects the probability distribution of alleles in the next generation.
Suppose an allele has frequency p1. We would like to see how much the allele frequency can change in the next
generation. Let p2 be the allele frequency in the second generation. Tis probability, p2 , is a random variable, so it has
an expected value and standard deviation. One can show that the mean μ and standard deviation  of this random
variable are:
p1 (1 — p1)
μ = p1 and = .
2N
Question 5
a. Suppose that the data are bell shaped. How much data lies within two standard deviations of the mean? Explain
your answer.
b. Suppose that the allele frequency p1 = 0.5 and the population size N = 25 (an accurate estimate of the
population size of panthers in the early-mid-1990s). Now consider your percentage answer (from 5a above), y%.
For that y% of cases, the allele frequency of p2 is in what range?
c. Repeat the calculation in 5b above for population sizes 33, 100, and 1000. What does an increased population
size do to the range?
d. In words, summarize how population size afects the probability distribution of the trait in the next generation.

Wait
Now let’s consider how the population size afects the average rate at which alleles are lost from the population. Using
the proportion of an allele in the population, p, we can also determine the number of generations it takes for an allele
to become fxed or lost given the population size.
Te average time to fxation is:

—4N (1 — p) 1n(1 — p)
Tfxed = .
p

And the average time to loss is:

—4Np 1n(p)
Tlost = .
1—p

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Question 6
a. Calculate the average time, in generations, to fxation of an allele that starts at proportion 0.4 in populations of
sizes 25, 33, 100, and 1000.
b. Calculate the average time, in generations, to loss of an allele that starts at proportion 0.4 in populations of sizes
25, 33, 100, and 1000.
c. Calculate the average time, in generations, to loss of an allele that starts at proportion 0.1 in populations of sizes
25, 33, 100, and 1000.
Wait
So far we’ve focused on alleles that are neutral with respect to natural selection. Tat means that none of the alleles
we’ve considered is either benefcial or detrimental to the population in comparison to the other alleles for that gene/
locus. But just because an allele is not benefcial to the organism now, doesn’t mean it won’t be benefcial in the future of
an ever-changing dynamic environment. Tis is one of the reasons that maintaining many alleles in the population is
generally a good thing, and the high rate of allele loss in a small population is a bad thing.
Tere is one other signifcant reason that small populations run a greater risk when it comes to extinction. Understand-
ing this reason requires that we now consider alleles that are currently benefcial or detrimental to the population, and
this deals with the fact that small populations are forced into inbreeding.

Inbreeding
You probably already have a sense that inbreeding is bad. Tere is a social stigma against inbreeding in our human
species that is shared by essentially every human society in the world. But it turns out there is a clear biological basis
for this stigma. Inbreeding is usually detrimental to the health of ofspring. To understand why that’s true, we need to
return to our understanding of genes and alleles. Remember that genes make proteins. It is these proteins that make the
traits of an organism. So if a trait is determined by a single gene, there are two alleles that could potentially contribute to
that trait.
How do these alleles interact to make the trait of an organism?
Te way a trait is determined by the alleles for a gene depends on how the alleles, and the proteins they make, interact
with each other. Obviously, if an individual is homozygous for a gene/locus (i.e., having two of the same allele), that
allele determines the trait. If an individual is heterozygous for a gene/locus (i.e., having two diferent allele types), there
are two main possibilities: (1) Te alleles can both contribute to the trait, or (2) the alleles can interact in such a way
that only one allele determines the trait. Tis latter case is quite common, and is the case on which we will focus here.
In this case, we call the one allele that determines the trait the dominant allele. Te allele that does not contribute to
the trait is called recessive.
Tis pattern of dominance and recessiveness is the basis of a major problem of inbreeding. Mutations in genes cause
new alleles to come about, and these mutated alleles are often very bad for the individual organism. We call these
bad alleles deleterious. If this new deleterious allele is dominant, it is very likely to negatively afect the individual’s
reproduction, so that an individual is less likely to survive and reproduce, and so the allele will not be passed on to
future generations and will quickly disappear from the population. If the new detrimental allele is recessive, it will only
afect the trait if there are two copies of the deleterious recessive allele. When an allele afects a trait we say that allele
is expressed. Terefore, a deleterious recessive allele is only expressed when it is present as a homozygote. Te efects
of this deleterious recessive allele are hidden when it is present in a heterozygote. Tese deleterious recessive alleles
persist in populations and are rarely expressed unless they become very common in the population, because one of the
deleterious recessive alleles must be inherited from each parent in order for it to afect the trait. So what we fnd in
nature is that many rare deleterious recessive alleles exist at many genes/loci in any population.
Two close relatives are more likely to have the same genes than are two randomly chosen individuals in the population.
So when two close relatives mate, the ofspring tend to have more homozygous genes/loci than the ofspring of

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randomly chosen mates—inbreeding causes an increase in homozygosity. Tis increase in homozygosity also means that
inbreeding causes an increase in traits determined by deleterious recessive alleles.
Because the size of the Florida panther population is so small, all of the individuals are closely related and so are forced
into inbreeding.

Question 7
Let’s calculate the efect of inbreeding on the expression of rare deleterious alleles.
a. Consider a rare deleterious recessive allele for a specifc gene/locus. In this hypothetical population, the
deleterious recessive allele exists at a proportion of 0.01. In an ofspring with randomly chosen parents, what is
the probability that the ofspring will be homozygous for the deleterious recessive allele?
b. Now let’s consider that the Florida panther population has 20,000 genes/loci (this is a reasonable estimate, and
is about the number of genes that humans have). And let’s assume that for every gene/locus there is a deleterious
recessive allele that exists at a proportion of 0.01 in the population. If all mating is random, in the average
ofspring, how many of its genes/loci are homozygous for deleterious recessive alleles?
c. Now consider an ofspring with full-sibling (brother and sister) parents. In this ofspring, what is the probability
that the ofspring will be homozygous for the deleterious recessive allele? Note that full siblings share, on
average, 50% of their genes. So, in order to calculate this, consider that one allele in an ofspring is randomly
inherited from the population. Ten, given that the randomly inherited allele is the deleterious recessive allele,
we can say that there is the normal chance of inheriting the deleterious recessive allele due to randomness, plus
an increased chance that the other parent has the allele due to the fact that it is a full sibling of the other parent.
Tis added increased chance must take into account that there is a 50% chance that the other parent has one
copy of that allele due to relatedness, and the fact that that parent has two alleles, so there is a 50% chance they
pass on that deleterious recessive allele if they have it.
d. Now consider the same mating of full siblings in a Florida panther population with 20,000 genes/loci where
each gene/locus has a deleterious recessive allele that exists at a proportion of 0.01 in the population. On
average, how many of the ofspring’s 20,000 genes/loci are homozygous for deleterious recessive alleles?
e. Compare the results of 7b and 7d above and explain what this means about the efects of inbreeding.

Wait
Clearly inbreeding has a drastic efect on how many deleterious recessive alleles are afecting traits! Tis highlights
yet another major problem of small population size, and an incredibly serious problem in conservation biology.
Because inbreeding increases the likelihood of homozygosity, this last problem of inbreeding can be approximated
by measuring the amount of homozygosity. If inbreeding increases, the average proportion of genes/loci that are
homozygous in a species should also increase. Inbreeding can similarly be identifed by a corresponding decrease in
heterozygosity.

Question 8
Summarize the three major problems with population size.

Wait
We now have a good understanding of the problems that small populations pose for the conservation and preservation
of species. Tis all adds up to the conclusion that, as the remaining numbers of a threatened species decrease, the
probability of saving the population does not scale linearly with population size. Rather, as the population depletes, the
per-capita efort needed to save a population/species must increase. Te fact that it becomes increasingly difcult, per-
capita, to save a species as its population’s size decreases, is termed the extinction vortex (Gilpin and Soulé 1986). Tis
“vortex” tends to exhibit an increasing strength pulling the population towards extinction as the population size decreases.

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If we look at data for the Florida panther population, we fnd lots of evidence of the existence of an extinction
vortex. Te increased presence of homozygous deleterious recessive alleles and the overall loss of alleles have serious
efects on many characteristics of the panther population. One important trait is whether or not they have descended
testes. During mammalian sexual development, testes descend from inside the body into the scrotum, and if testes
do not descend, an animal is generally sterile. Te failure of one or both testes to descend is known as cryptorchidism.
Obviously a high proportion of sterile individuals will have an efect on the possibility of increasing population size.
Another important trait is atrial septal defects. Tese are defects in chambers of the heart that complicate blood fow
through the heart, making it more difcult to survive. An increase in heart defects will also obviously have an efect
on the possibility of increasing population size. In this population of Florida panthers, these traits were measured over
generations, as summarized in Table 1.

Table 1. Occurrence of deleterious traits in Florida panther population 1970–1995, with standard errors removed for simplicity (Johnson et al. 2010).
Heritage Group Average Heterozygosity Proportion of Males Proportion with Atrial
Cryptorchid Septal Defects
1970–1984 0.231 0.33 0.33
1985–1989 0.208 0.50 0.16
1990–1995 0.190 0.63 0.21

Question 9
Summarize the observed trends in the traits in Table 1.

Question 10
It turns out that the Florida panther is closely related to a population of panthers (cougars) that still exist in Texas. In
fact, the Florida population and the Texas population used to be part of one continuous population of panthers. So
it is highly likely that they could and would interbreed. Based on the information available in the mid-1990s, some
conservation biologists believed that the only way to save the population of Florida panthers would be to introduce
several Texas cougars into Florida to revitalize the population of Florida panthers. Do you think this is a good idea?
Also consider factors beyond probability that may infuence society’s decision on this matter.

Wait
It turns out that conservation managers decided to introduce eight female Texas cougars into the population of Florida
panthers in 1995 (hence the reasoning for our doing many of the previous calculations for population size 25 and 33).
Aside from simply increasing population size, this increase in genetic variation had notable efects on important traits
in the Florida panther, as summarized in Table 2.

Table 2. Occurrence of deleterious traits in Florida panther population 1970–2007, with standard errors removed for simplicity (Johnson et al. 2010).
Heritage Group Total Number of Individuals Average Proportion of Male Proportion with
Observed Over Time Period Heterozygosity Cryptorchid Atrial Septal Defects
Prior to Texas Cougar Introduction
1970–1984 33 0.231 0.33 0.33
1985–1989 37 0.208 0.50 0.16
1990–1995 62 0.190 0.63 0.21
After Texas Cougar Introduction
1996–1998 67 0.220 0.54 0.06
1999–2001 102 0.224 0.42 0.07
2002–2004 139 0.226 0.23 0.06
2005–2007 116 0.240 0.12 0.09

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Question 11
a. Summarize the change in the traits in Table 2 after the introduction of the Texas cougars.
b. After seeing these data, do you think the introduction of the Texas cougars was a good idea?

Wait

Some Extra Panther Probability Problems

Question 12
Use the data in Table 2 to answer the following questions. While the “Total Number of Individuals Observed Over
Time Period” is not necessarily the same as the population size (because it considers individuals present in the
population over a time range rather than a specifc point in time), it is highly correlated with the population size, and
for our purposes we can use these numbers as the population sizes where needed.
a. Suppose in the early 1990s a doctor volunteers to help one panther with its atrial septal heart condition. She
will help the frst panther she fnds that is in need of help. What is the probability that the frst, second, or third
panther she fnds has this condition?
b. Suppose the son of the early 1990s doctor now volunteers his time to help one panther with this condition
during the time period 2005–2007. He will help the frst panther he fnds that is in need of help. What is the
probability that the frst, second, third, fourth, or ffth panther he fnds has this condition?
c. Interpret the diference in the results of the previous two problems.
d. In your calculations for the doctor and her son, did population size matter? If so, explain how you used
the population size. If not, explain why it didn’t matter, but mention the signifcance in terms of how the
introduction of Texas cougars helped.

Literature Cited
Gilpin, M.E., and Soulé, M.E. (1986) Minimum viable populations: processes of species extinction. In: Soulé, M.E.
(ed,) Conservation Biology: Te Science of Scarcity and Diversity. Sinauer, Sunderland, pp. 19–34.
Johnson, W.E., Onorato, D.P., Roelke, M.E., Land, E.D., Cunningham, M., Belden, R.C., McBride, R., Jansen, D.,
Lotz, M., Shindle, D., Howard, J., Wildt, D.E., Penfold, L.M., Hostetler, J.A., Oli, M.K., and O’Brien, S.J.
(2010) Genetic restoration of the Florida panther. Science 329: 1641–1645.
Packer, C. (2010) Genetics. A bit of Texas in Florida. Science 329: 1606–1607.

Case copyright held by the National Center for Case Study Teaching in Science, University at Buffalo, State University of New York.
Origi-nally published August 15, 2013. Please see our usage guidelines, which outline our policy concerning permissible reproduction of
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